RE: revamping the Apache cTAKES website
Check out a mockup of a new website proposal: http://svn.apache.org/repos/asf/ctakes/site/new/index.html Based off bootstrap (Idea borrowed from the Spark folks..). Couple of key pieces of info: - 10% of visitors are on mobile/tablets - The most currently visited pages are: downloads.cgi, gettingstarted.html. I suggest we focus our attention on those 2 items. (Putting a Downloads link right on the front page, etc.) svn co http://svn.apache.org/repos/asf/ctakes/site/new if you want to checkout the code of the site. --Pei -Original Message- From: John Green [mailto:john.travis.gr...@gmail.com] Sent: Friday, December 05, 2014 6:34 PM To: dev@ctakes.apache.org Cc: dev@ctakes.apache.org Subject: RE: revamping the Apache cTAKES website I would like to second the bootstrap recommendation, with the additional recommendation of django for the backend. It is an amazing platform for rapid development and easy updating. JG — Sent from Mailbox On Fri, Dec 5, 2014 at 12:15 PM, Savova, Guergana guergana.sav...@childrens.harvard.edu wrote: There are now 4 volunteers: Michelle Chen Pei Chen Sean Finan Guergana Savova --Guergana -Original Message- From: Savova, Guergana [mailto:guergana.sav...@childrens.harvard.edu] Sent: Friday, December 05, 2014 11:56 AM To: dev@ctakes.apache.org Subject: RE: revamping the Apache cTAKES website Wonderful, thank you, Michelle! There will be a flurry of emails the week of Dec 15 followed by actual work, so book your calendar if possible... --Guergana -Original Message- From: Michelle Chen [mailto:michelle1919c...@gmail.com] Sent: Friday, December 05, 2014 11:48 AM To: dev@ctakes.apache.org Subject: Re: revamping the Apache cTAKES website Hello Guergana, I don't know that much about cTakes, but would be interested in contributing to the effort. I'm not sure if there is an interest in matching the website design of other Apache projects, but it seems that the two main designs that are being used from my arbitrary search on http://projects.apache.org/indexes/alpha.html is 1. the current design that cTakes is using and 2. a Bootstrap approach. I've done a little bit of work on Bootstrap and would be interested in helping with that. Let me know how I can be helpful. Sincerely, Michelle Chen :) Be strong and of good courage; do not be afraid, nor be dismayed, for the Lord your God is with you wherever you go. ~Joshua 1:9 On Fri, Dec 5, 2014 at 11:21 AM, Savova, Guergana guergana.sav...@childrens.harvard.edu wrote: cTAKES-ers, we would like to start working on updating the Apache cTAKES website - some of the information there is already stale and needs refreshing. Do you have ideas on website design, content, etc.? Would you like to contribute to the effort? We are planning to start working on the website the week of Dec 15. Cheers, --Guergana
RE: revamping the Apache cTAKES website
Anyway, a pretty amazing fresh start, thanks Pei -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Monday, December 15, 2014 4:33 PM To: dev@ctakes.apache.org Subject: RE: revamping the Apache cTAKES website Check out a mockup of a new website proposal: http://svn.apache.org/repos/asf/ctakes/site/new/index.html Based off bootstrap (Idea borrowed from the Spark folks..). Couple of key pieces of info: - 10% of visitors are on mobile/tablets - The most currently visited pages are: downloads.cgi, gettingstarted.html. I suggest we focus our attention on those 2 items. (Putting a Downloads link right on the front page, etc.) svn co http://svn.apache.org/repos/asf/ctakes/site/new if you want to checkout the code of the site. --Pei -Original Message- From: John Green [mailto:john.travis.gr...@gmail.com] Sent: Friday, December 05, 2014 6:34 PM To: dev@ctakes.apache.org Cc: dev@ctakes.apache.org Subject: RE: revamping the Apache cTAKES website I would like to second the bootstrap recommendation, with the additional recommendation of django for the backend. It is an amazing platform for rapid development and easy updating. JG — Sent from Mailbox On Fri, Dec 5, 2014 at 12:15 PM, Savova, Guergana guergana.sav...@childrens.harvard.edu wrote: There are now 4 volunteers: Michelle Chen Pei Chen Sean Finan Guergana Savova --Guergana -Original Message- From: Savova, Guergana [mailto:guergana.sav...@childrens.harvard.edu] Sent: Friday, December 05, 2014 11:56 AM To: dev@ctakes.apache.org Subject: RE: revamping the Apache cTAKES website Wonderful, thank you, Michelle! There will be a flurry of emails the week of Dec 15 followed by actual work, so book your calendar if possible... --Guergana -Original Message- From: Michelle Chen [mailto:michelle1919c...@gmail.com] Sent: Friday, December 05, 2014 11:48 AM To: dev@ctakes.apache.org Subject: Re: revamping the Apache cTAKES website Hello Guergana, I don't know that much about cTakes, but would be interested in contributing to the effort. I'm not sure if there is an interest in matching the website design of other Apache projects, but it seems that the two main designs that are being used from my arbitrary search on http://projects.apache.org/indexes/alpha.html is 1. the current design that cTakes is using and 2. a Bootstrap approach. I've done a little bit of work on Bootstrap and would be interested in helping with that. Let me know how I can be helpful. Sincerely, Michelle Chen :) Be strong and of good courage; do not be afraid, nor be dismayed, for the Lord your God is with you wherever you go. ~Joshua 1:9 On Fri, Dec 5, 2014 at 11:21 AM, Savova, Guergana guergana.sav...@childrens.harvard.edu wrote: cTAKES-ers, we would like to start working on updating the Apache cTAKES website - some of the information there is already stale and needs refreshing. Do you have ideas on website design, content, etc.? Would you like to contribute to the effort? We are planning to start working on the website the week of Dec 15. Cheers, --Guergana
RE: Problem running cTakes-clinical pipeline -- AggregatePlaintextFastUMLSProcessor.xml
Hi Yu, Also do you know is there any command line I can run to annotate like a thousand files automatically rather than copy and paster. You could try the CPE gui : bin/runctakesCPE.sh Sean From: Liang, Yu [mailto:yu.li...@nyumc.org] Sent: Monday, December 15, 2014 4:51 PM To: dev@ctakes.apache.org Subject: Problem running cTakes-clinical pipeline -- AggregatePlaintextFastUMLSProcessor.xml Hi Yu, I think this is a current limitation in cTAKES. I think it has to do with negation not detecting if the line breaks are separating the sentences. Would you mind forwarding the example to dev@ctakes.apache.orgmailto:dev@ctakes.apache.org? I think Tim and others may be working on this issue. --Pei On Mon, Dec 15, 2014 at 3:54 PM, Liang, Yu yu.li...@nyumc.orgmailto:yu.li...@nyumc.org wrote: On Dec 15, 2014, at 2:58 PM, Liang, Yu yu.li...@nyumc.orgmailto:yu.li...@nyumc.org wrote: Hi Pei Chen, Could you please look at the following example I run, I think the result is not accurate. The polarity of illness is -1 but for fever, vomiting, diarrhea,and pain are all +1. Also do you know is there any command line I can run to annotate like a thousand files automatically rather than copy and paster. Yu Liang [cid:DF19883E-B993-4CD0-90BD-F285A3C1A5A3@wireless.nyumc.org] Yu Liang CHIBI
Re: revamping the Apache cTAKES website
Looks great. +1 On Dec 15, 2014, at 4:29 PM, Chen, Pei pei.c...@childrens.harvard.edu wrote: Check out a mockup of a new website proposal: http://svn.apache.org/repos/asf/ctakes/site/new/index.html Based off bootstrap (Idea borrowed from the Spark folks..). Couple of key pieces of info: - 10% of visitors are on mobile/tablets - The most currently visited pages are: downloads.cgi, gettingstarted.html. I suggest we focus our attention on those 2 items. (Putting a Downloads link right on the front page, etc.) svn co http://svn.apache.org/repos/asf/ctakes/site/new if you want to checkout the code of the site. --Pei -Original Message- From: John Green [mailto:john.travis.gr...@gmail.com] Sent: Friday, December 05, 2014 6:34 PM To: dev@ctakes.apache.org Cc: dev@ctakes.apache.org Subject: RE: revamping the Apache cTAKES website I would like to second the bootstrap recommendation, with the additional recommendation of django for the backend. It is an amazing platform for rapid development and easy updating. JG — Sent from Mailbox On Fri, Dec 5, 2014 at 12:15 PM, Savova, Guergana guergana.sav...@childrens.harvard.edu wrote: There are now 4 volunteers: Michelle Chen Pei Chen Sean Finan Guergana Savova --Guergana -Original Message- From: Savova, Guergana [mailto:guergana.sav...@childrens.harvard.edu] Sent: Friday, December 05, 2014 11:56 AM To: dev@ctakes.apache.org Subject: RE: revamping the Apache cTAKES website Wonderful, thank you, Michelle! There will be a flurry of emails the week of Dec 15 followed by actual work, so book your calendar if possible... --Guergana -Original Message- From: Michelle Chen [mailto:michelle1919c...@gmail.com] Sent: Friday, December 05, 2014 11:48 AM To: dev@ctakes.apache.org Subject: Re: revamping the Apache cTAKES website Hello Guergana, I don't know that much about cTakes, but would be interested in contributing to the effort. I'm not sure if there is an interest in matching the website design of other Apache projects, but it seems that the two main designs that are being used from my arbitrary search on http://projects.apache.org/indexes/alpha.html is 1. the current design that cTakes is using and 2. a Bootstrap approach. I've done a little bit of work on Bootstrap and would be interested in helping with that. Let me know how I can be helpful. Sincerely, Michelle Chen :) Be strong and of good courage; do not be afraid, nor be dismayed, for the Lord your God is with you wherever you go. ~Joshua 1:9 On Fri, Dec 5, 2014 at 11:21 AM, Savova, Guergana guergana.sav...@childrens.harvard.edu wrote: cTAKES-ers, we would like to start working on updating the Apache cTAKES website - some of the information there is already stale and needs refreshing. Do you have ideas on website design, content, etc.? Would you like to contribute to the effort? We are planning to start working on the website the week of Dec 15. Cheers, --Guergana
Re: revamping the Apache cTAKES website
this is gorgeous ! Thanks pei ! i let the bigtop folks know as well ! On Mon, Dec 15, 2014 at 6:21 PM, Murali mmin...@gmail.com wrote: Looks great. +1 On Dec 15, 2014, at 4:29 PM, Chen, Pei pei.c...@childrens.harvard.edu wrote: Check out a mockup of a new website proposal: http://svn.apache.org/repos/asf/ctakes/site/new/index.html Based off bootstrap (Idea borrowed from the Spark folks..). Couple of key pieces of info: - 10% of visitors are on mobile/tablets - The most currently visited pages are: downloads.cgi, gettingstarted.html. I suggest we focus our attention on those 2 items. (Putting a Downloads link right on the front page, etc.) svn co http://svn.apache.org/repos/asf/ctakes/site/new if you want to checkout the code of the site. --Pei -Original Message- From: John Green [mailto:john.travis.gr...@gmail.com] Sent: Friday, December 05, 2014 6:34 PM To: dev@ctakes.apache.org Cc: dev@ctakes.apache.org Subject: RE: revamping the Apache cTAKES website I would like to second the bootstrap recommendation, with the additional recommendation of django for the backend. It is an amazing platform for rapid development and easy updating. JG — Sent from Mailbox On Fri, Dec 5, 2014 at 12:15 PM, Savova, Guergana guergana.sav...@childrens.harvard.edu wrote: There are now 4 volunteers: Michelle Chen Pei Chen Sean Finan Guergana Savova --Guergana -Original Message- From: Savova, Guergana [mailto:guergana.sav...@childrens.harvard.edu] Sent: Friday, December 05, 2014 11:56 AM To: dev@ctakes.apache.org Subject: RE: revamping the Apache cTAKES website Wonderful, thank you, Michelle! There will be a flurry of emails the week of Dec 15 followed by actual work, so book your calendar if possible... --Guergana -Original Message- From: Michelle Chen [mailto:michelle1919c...@gmail.com] Sent: Friday, December 05, 2014 11:48 AM To: dev@ctakes.apache.org Subject: Re: revamping the Apache cTAKES website Hello Guergana, I don't know that much about cTakes, but would be interested in contributing to the effort. I'm not sure if there is an interest in matching the website design of other Apache projects, but it seems that the two main designs that are being used from my arbitrary search on http://projects.apache.org/indexes/alpha.html is 1. the current design that cTakes is using and 2. a Bootstrap approach. I've done a little bit of work on Bootstrap and would be interested in helping with that. Let me know how I can be helpful. Sincerely, Michelle Chen :) Be strong and of good courage; do not be afraid, nor be dismayed, for the Lord your God is with you wherever you go. ~Joshua 1:9 On Fri, Dec 5, 2014 at 11:21 AM, Savova, Guergana guergana.sav...@childrens.harvard.edu wrote: cTAKES-ers, we would like to start working on updating the Apache cTAKES website - some of the information there is already stale and needs refreshing. Do you have ideas on website design, content, etc.? Would you like to contribute to the effort? We are planning to start working on the website the week of Dec 15. Cheers, --Guergana -- jay vyas
Re: revamping the Apache cTAKES website
the template was borrowed from spark... we should put in our own design/css/layout/skin to suit our needs. Perhaps Michelle or others familiar with bootstrap could help us out here? On Mon, Dec 15, 2014 at 7:32 PM, jay vyas jayunit100.apa...@gmail.com wrote: this is gorgeous ! Thanks pei ! i let the bigtop folks know as well ! On Mon, Dec 15, 2014 at 6:21 PM, Murali mmin...@gmail.com wrote: Looks great. +1 On Dec 15, 2014, at 4:29 PM, Chen, Pei pei.c...@childrens.harvard.edu wrote: Check out a mockup of a new website proposal: http://svn.apache.org/repos/asf/ctakes/site/new/index.html Based off bootstrap (Idea borrowed from the Spark folks..). Couple of key pieces of info: - 10% of visitors are on mobile/tablets - The most currently visited pages are: downloads.cgi, gettingstarted.html. I suggest we focus our attention on those 2 items. (Putting a Downloads link right on the front page, etc.) svn co http://svn.apache.org/repos/asf/ctakes/site/new if you want to checkout the code of the site. --Pei -Original Message- From: John Green [mailto:john.travis.gr...@gmail.com] Sent: Friday, December 05, 2014 6:34 PM To: dev@ctakes.apache.org Cc: dev@ctakes.apache.org Subject: RE: revamping the Apache cTAKES website I would like to second the bootstrap recommendation, with the additional recommendation of django for the backend. It is an amazing platform for rapid development and easy updating. JG — Sent from Mailbox On Fri, Dec 5, 2014 at 12:15 PM, Savova, Guergana guergana.sav...@childrens.harvard.edu wrote: There are now 4 volunteers: Michelle Chen Pei Chen Sean Finan Guergana Savova --Guergana -Original Message- From: Savova, Guergana [mailto:guergana.sav...@childrens.harvard.edu] Sent: Friday, December 05, 2014 11:56 AM To: dev@ctakes.apache.org Subject: RE: revamping the Apache cTAKES website Wonderful, thank you, Michelle! There will be a flurry of emails the week of Dec 15 followed by actual work, so book your calendar if possible... --Guergana -Original Message- From: Michelle Chen [mailto:michelle1919c...@gmail.com] Sent: Friday, December 05, 2014 11:48 AM To: dev@ctakes.apache.org Subject: Re: revamping the Apache cTAKES website Hello Guergana, I don't know that much about cTakes, but would be interested in contributing to the effort. I'm not sure if there is an interest in matching the website design of other Apache projects, but it seems that the two main designs that are being used from my arbitrary search on http://projects.apache.org/indexes/alpha.html is 1. the current design that cTakes is using and 2. a Bootstrap approach. I've done a little bit of work on Bootstrap and would be interested in helping with that. Let me know how I can be helpful. Sincerely, Michelle Chen :) Be strong and of good courage; do not be afraid, nor be dismayed, for the Lord your God is with you wherever you go. ~Joshua 1:9 On Fri, Dec 5, 2014 at 11:21 AM, Savova, Guergana guergana.sav...@childrens.harvard.edu wrote: cTAKES-ers, we would like to start working on updating the Apache cTAKES website - some of the information there is already stale and needs refreshing. Do you have ideas on website design, content, etc.? Would you like to contribute to the effort? We are planning to start working on the website the week of Dec 15. Cheers, --Guergana -- jay vyas
UMLS Integration
Hi All, I downloaded UMLS resource, to use them offline by loading in mysql. I followed them which are mentioned to load data into mysql. But I am unable to do it show error Loading MetamorphoSys ... [Please be patient and wait for MetamorphoSys to begin] java.util.zip.ZipException: invalid LOC header (bad signature) at java.util.zip.ZipFile.read(Native Method) at java.util.zip.ZipFile.access$1400(Unknown Source) at java.util.zip.ZipFile$ZipFileInputStream.read(Unknown Source) at java.util.zip.ZipFile$ZipFileInflaterInputStream.fill(Unknown Source) at java.util.zip.InflaterInputStream.read(Unknown Source) at java.util.zip.InflaterInputStream.read(Unknown Source) at java.util.zip.CheckedInputStream.read(Unknown Source) at java.util.zip.GZIPInputStream.readUByte(Unknown Source) at java.util.zip.GZIPInputStream.readUShort(Unknown Source) at java.util.zip.GZIPInputStream.readHeader(Unknown Source) at java.util.zip.GZIPInputStream.init(Unknown Source) at gov.nih.nlm.umls.meta.io.RRFMetadataInputStream.openSourceFile(RRFMetadataInputStream.java:390) at gov.nih.nlm.umls.meta.io.RRFConceptInputStream.open(RRFConceptInputStream.java:175) at gov.nih.nlm.umls.meta.io.RRFMetathesaurusInputStream.open(RRFMetathesaurusInputStream.java:125) at gov.nih.nlm.umls.mmsys.io.RRFMetamorphoSysInputStream.open(RRFMetamorphoSysInputStream.java:629) at gov.nih.nlm.umls.mmsys.subset.gui.MetamorphoSysGUI.validateGUIConfigurables(MetamorphoSysGUI.java:1097) at gov.nih.nlm.umls.mmsys.subset.gui.BeginSubsetAction.actionPerformed(BeginSubsetAction.java:110) at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.setPressed(Unknown Source) at javax.swing.AbstractButton.doClick(Unknown Source) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source) at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source) at java.awt.Component.processMouseEvent(Unknown Source) at javax.swing.JComponent.processMouseEvent(Unknown Source) at java.awt.Component.processEvent(Unknown Source) at java.awt.Container.processEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$200(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) Please help to slove this issue. Thaks in advance. Regards, Praveen.
